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- PDB-3nq3: Bovine beta-lactoglobulin complex with capric acid -

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Basic information

Entry
Database: PDB / ID: 3nq3
TitleBovine beta-lactoglobulin complex with capric acid
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN / beta-lactoglobulin / lipocalin / bovine milk / capric acid / decanoic acid / fatty acid
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DECANOIC ACID / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLoch, J.I. / Lewinski, K.
CitationJournal: J.Mol.Recognit. / Year: 2011
Title: Two modes of fatty acid binding to bovine beta-lactoglobulin-crystallographic and spectroscopic studies
Authors: Loch, J.I. / Polit, A. / Gorecki, A. / Bonarek, P. / Kurpiewska, K. / Dziedzicka-Wasylewska, M. / Lewinski, K.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6014
Polymers18,3011
Non-polymers3003
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.500, 53.500, 112.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18301.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: milk / References: UniProt: P02754
#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.34M trisodium citrate, 0.1M Tris-HCl buffer, 1mM capric acid in 96% ethanol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD TITAN CCD / Detector: CCD / Date: Oct 3, 2009 / Details: Atlas detector 135mm
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 15155 / % possible obs: 99.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2172 / % possible all: 100

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.2.0005refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BSY

1bsy


Resolution: 1.9→9.96 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.345 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2893 769 5.1 %RANDOM
Rwork0.23831 ---
obs0.24082 14348 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.629 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→9.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 19 115 1414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221369
X-RAY DIFFRACTIONr_angle_refined_deg1.9212.0031863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4635177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53527.04961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79415264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.629153
X-RAY DIFFRACTIONr_chiral_restr0.1320.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021007
X-RAY DIFFRACTIONr_nbd_refined0.240.2658
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.217
X-RAY DIFFRACTIONr_mcbond_it1.2561.5859
X-RAY DIFFRACTIONr_mcangle_it2.04721368
X-RAY DIFFRACTIONr_scbond_it2.5393564
X-RAY DIFFRACTIONr_scangle_it3.9614.5487
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 42 -
Rwork0.305 1005 -
obs--99.9 %

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